Closest phylogenetic relatives are Indochinese Chiromyscus and Dacnomys; among Sundaic genera, Niviventer shares dental derivations with Berylmys, Leopoldamys, and Maxomys (Musser, 1981b; Musser and Newcomb, 1983). Analyses of chromosomal data postulated similarities among Niviventer, Lenothrix, and possibly Maxomys, and an origin from a common ancestor (Gadi and Sharma, 1983). Analyses of allozymic and morphological data for Malay Peninsula species demonstrated substantial separation from Rattus, with which Niviventer had been merged (Ellerman, 1941, 1961; see history in Musser, 1981b), and alliance with Lenothrix in protein variation, but equivocal affinities in morphological context (Chan et al., 1979). Spermatozoal morphology equivocal in assessing phylogenetic relationships (Breed and Yong, 1986). Cladistic analysis of DNA sequence from LINE-1 elements placed Niviventer and Leopoldamys together in a clade (our Dacnomys Division) separate from another containing Rattus, Berylmys, Sundamys, and Bandicota (our Rattus Division), and a third with only Maxomys (Verneau et al., 1997, 1998). These kinship patterns are also supported by albumin immunology (Watts and Baverstock, 1994b), DNA/DNA hybridization (Chevret, 1994 [cited in Verneau, 1997]), and generally by cranial and dental traits (Musser and Newcomb, 1983). Pavlinov et al. (1995a) listed Niviventer in a Dacnomys Section of a more inclusive Rattus Group. Phallic morphology of three Chinese taxa described by Yang and Fang (1988) in context of assessing phylogenetic relationships among Chinese murines.

Recent multivariate analyses of morphometric traits for samples of Niviventer (Musser and Lunde, ms) substantiate the limits of 11 species (N. andersoni, N. brahma, N. coninga, N. cremoriventer, N. culturatus, N. eha, N. excelsior, N. hinpoon, N. langbianis, N. lepturus, and N. niviventer) that were considered clearly defined using morphological criteria (Corbet and Hill, 1992; Musser, 1981b; Musser and Newcomb, 1983), and helped formulate definitions of N. confucianus, N. fulvescens, and N. tenaster in the Indochinese region and N. cameroni, N. rapit,and N. fraternus on the Sunda Shelf. The analyses also identify an undescribed species from N Burma and a new genus related to Niviventer from C Laos; descriptions of these taxa are being prepared by Musser and colleagues.

Niviventer is represented by fossils found in China and Thailand. Evolutionary history of N. andersoni and N. confucianus in S China extends back to early Pleistocene as documented by fossils recovered from cave sediments in the Sichuan-Guizhou region (Zheng, 1993); fragments found in the same region, but at late Pliocene to early Pleistocene horizons were described as N. preconfucianus (Zheng, 1993). Both N. confucianus and N. preconfucianus were discovered in Pleistocene fissure deposits in the Shandong region, with the latter found in earlier horizons (Zheng et al., 1997). Late or middle Pleistocene cave layers in Guangxi Province of S China yielded three molar classes, identified as Niviventer sp. 1-3 (Chen et al., 2002). From middle Pleistocene cave sediments in Thailand come examples of extant N. fulvescens and extinct N. gracilis (Chaimanee, 1998). The earliest record of Niviventer is from 4.5 million-year-old strata (early Pliocene) in the Yushe Basin of Shanxi Province, which indicates an early origin for the Dacnomys Division (L. J. Flynn, in litt., 2003).